I have had a look at this, and although i can indeed reproduce it, I can't do anything about it. PHP seems to be not generating JMP instructions on the right line. With the attached file, the VLD tool produces:

$ php -dvld.active=1 -dextension=vld.so /tmp/2179.php 
Finding entry points
Branch analysis from position: 0
1 jumps found. (Code = 62) Position 1 = -2
filename:       /tmp/2179.php
function name:  (null)
number of ops:  1
compiled vars:  none
line      #* E I O op                           fetch          ext  return  operands
-------------------------------------------------------------------------------------
   29     0  E > > RETURN                                                   1

branch: #  0; line:    29-   29; sop:     0; eop:     0; out0:  -2
path #1: 0, 
Function getbyfilename:
Finding entry points
Branch analysis from position: 0
2 jumps found. (Code = 43) Position 1 = 2, Position 2 = 15
Branch analysis from position: 2
2 jumps found. (Code = 43) Position 1 = 4, Position 2 = 14
Branch analysis from position: 4
1 jumps found. (Code = 79) Position 1 = -2
Branch analysis from position: 14
1 jumps found. (Code = 42) Position 1 = 15
Branch analysis from position: 15
1 jumps found. (Code = 62) Position 1 = -2
Branch analysis from position: 15
filename:       /tmp/2179.php
function name:  getByFilename
number of ops:  17
compiled vars:  !0 = $this_file_format, !1 = $file_format
line      #* E I O op                           fetch          ext  return  operands
-------------------------------------------------------------------------------------
    5     0  E >   EXT_STMT                                                 
          1      > JMPZ                                                     <true>, ->15
    7     2    >   EXT_STMT                                                 
          3      > JMPZ                                                     <false>, ->14
    9     4    >   EXT_STMT                                                 
          5        ASSIGN                                                   !0, !1
   10     6        EXT_STMT                                                 
          7      > EXIT                                                     
   11     8*       EXT_STMT                                                 
          9*       EXIT                                                     
   12    10*       EXT_STMT                                                 
         11*       NEW                                              $3      'Exception'
         12*       DO_FCALL                                      0          
         13*       THROW                                         0          $3
         14    > > JMP                                                      ->15
   16    15    >   EXT_STMT                                                 
         16      > RETURN                                                   null

branch: #  0; line:     5-    5; sop:     0; eop:     1; out0:   2; out1:  15
branch: #  2; line:     7-    7; sop:     2; eop:     3; out0:   4; out1:  14
branch: #  4; line:     9-   10; sop:     4; eop:     7; out0:  -2
branch: # 14; line:    12-   12; sop:    14; eop:    14; out0:  15
branch: # 15; line:    16-   16; sop:    15; eop:    16; out0:  -2
path #1: 0, 2, 4, 
path 0000002: 0, 2, 14, 15, 
path 0000003: 0, 15, 
End of function getbyfilename

Function getbyfilename2:
Finding entry points
Branch analysis from position: 0
2 jumps found. (Code = 43) Position 1 = 2, Position 2 = 7
Branch analysis from position: 2
2 jumps found. (Code = 43) Position 1 = 4, Position 2 = 6
Branch analysis from position: 4
1 jumps found. (Code = 42) Position 1 = 7
Branch analysis from position: 7
1 jumps found. (Code = 62) Position 1 = -2
Branch analysis from position: 6
Branch analysis from position: 7
filename:       /tmp/2179.php
function name:  getByFilename2
number of ops:  9
compiled vars:  !0 = $this_file_format, !1 = $file_format
line      #* E I O op                           fetch          ext  return  operands
-------------------------------------------------------------------------------------
   20     0  E >   EXT_STMT                                                 
          1      > JMPZ                                                     <true>, ->7
   22     2    >   EXT_STMT                                                 
          3      > JMPZ                                                     <false>, ->6
   24     4    >   EXT_STMT                                                 
          5        ASSIGN                                                   !0, !1
          6    > > JMP                                                      ->7
   28     7    >   EXT_STMT                                                 
          8      > RETURN                                                   null

branch: #  0; line:    20-   20; sop:     0; eop:     1; out0:   2; out1:   7
branch: #  2; line:    22-   22; sop:     2; eop:     3; out0:   4; out1:   6
branch: #  4; line:    24-   24; sop:     4; eop:     5; out0:   6
branch: #  6; line:    24-   24; sop:     6; eop:     6; out0:   7
branch: #  7; line:    28-   28; sop:     7; eop:     8; out0:  -2
path #1: 0, 2, 4, 6, 7, 
path 0000002: 0, 2, 6, 7, 
path 0000003: 0, 7, 
End of function getbyfilename2

In the first function getByFilename the JMP on line 12/op 14, should really have been generated for line 14 where the else is, and similarly for the JMP on line 24/op 6 in the second function, which should be on line 26. I don't know whether it is possible to fix this in PHP, but I will have a talk with some of the other engine folks about it.

<?php

function getByFilename()
{
    if (true) {
        if (
            false
        ) {
            $this_file_format = $file_format; // will be shown as not covered
            exit;   // will be shown as not covered
            die;    // will be shown as not covered
            throw new Exception(); // will be shown as covered because it's the last line in the block
        }
    } else {    // the else is crucial even when it's not actually called. and when it's empty. When removed, the coverage bug stops happening.
    }
}

function getByFilename2()
{
    if (true) {
        if (
            false
        ) {
            $this_file_format = $file_format; // will be shown as covered because it's the last (=only) line in the block
        }
    } else {    // the else is crucial even when it's not actually called. and when it's empty. When removed, the coverage bug stops happening.
    }
}

This is going to be fixed in PHP 8.2.9: https://github.com/php/php-src/pull/11598#pullrequestreview-1514703137 — so I'll be closing this issue.

Thank you @derick! Much appreciated.